RetrogeneDB ID: retro_nleu_1993

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:7439281..7440014(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ATG4A
• Ensembl ID: ENSNLEG00000014016
• Aliases: None
• Description: None

Sequence

>retro_nleu_1993
GTTAACAAAAAACTCGCTTTATTTGATGAATGGAATTCCTTGGCTCTTTATGTTTCAATGGATAACACAGTGGTCATTGA
AGATATCAAAAAATGTGTTATGTCCTTCCCTTGAGTGCTTACACAGACCGTGACAGGCCTCCGGATTCTCTGACTGCTTT
AAACTAGAGTAAGGGCAACTCCGCCTACTGCCTAGCCTGGAAACCCCTGCTGCTTATTGTGCCCCTTTGCCTGGGCATAA
ACCAAATCAACCCTGTCTATGTTGATGCATTCAAAGAGTGTTTTAAGATGACACAGTCTTTAGGGGCATTAGGAGAAAAC
CAAATAACGCCTATTGTTTCAAAGAATTCTTAGGTGATAAGCTCATCTTCCTGGACCCTCACACAACCCAGACCTTTGTC
AACACTGAAGAGAATGAAACGGTTGATGATCAGACTTTCCATTACCTGCAGTCCCCACAGCAAATGAACATGCTCAACCT
GGATCCTTCAGTTGCACTGGGATTTTTCTGAAAATAAGAAAAAGACTTTAATAACTGGCATAGCCTTGTTCAGAAGGAAA
TTCTAAAGGAGCATTTGAACATGTTTGAATTGATTCAGAAACATCCATTGCACTGGCCTCGCCTTGTACCTCCAGCCAAG
CCAGAAGTGACAACCACTGGGGCATAATTCATTGACTCTACTGAACAACTGGATGAGTTTGATCTGGAGGAAGATTTTGA
GATTCTGAATGTG

Alignment

ORF - retro_nleu_1993 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.62 %
• Parental protein coverage: 61.56 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLKKLALFDEWNSLAVYVSMDNTVVIEDIKK-MCCVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKP
          V.KKLALFDEWNSLA.YVSMDNTVVIEDIKK.MC.VLPLSA.T..DRPPDSLTA.N.SKG.SAYC.AWKP
Retrocopy VNKKLALFDEWNSLALYVSMDNTVVIEDIKK<MCYVLPLSAYTDRDRPPDSLTALN*SKGNSAYCLAWKP

Parental  LLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGG-KPNNAYYFIGFLGDELIFLDPHTTQTFVDTEE
          LLLIVPL.LGINQINPVYVDAFKECFKM.QSLGALG..KPNNAY.F..FLGD.LIFLDPHTTQTFV.TEE
Retrocopy LLLIVPLCLGINQINPVYVDAFKECFKMTQSLGALGE<KPNNAYCFKEFLGDKLIFLDPHTTQTFVNTEE

Parental  NGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHWPP
          N.TV.DQTFH.LQSPQ.MN.LNLDPSVALGFF.K.EKDF.NW.SLVQKEILKE.L.MFEL.QKHP.HWP.
Retrocopy NETVDDQTFHYLQSPQQMNMLNLDPSVALGFF*K*EKDFNNWHSLVQKEILKEHLNMFELIQKHPLHWPR

Parental  FVPPAKPEVTTTGAEFIDSTEQLEEFDLEEDFEILSV
          .VPPAKPEVTTTGA.FIDSTEQL.EFDLEEDFEIL.V
Retrocopy LVPPAKPEVTTTGA*FIDSTEQLDEFDLEEDFEILNV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1993 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000002971	1 retrocopy	retro_ggor_2935,
Mus musculus	ENSMUSG00000079418	1 retrocopy	retro_mmus_2283,
Nomascus leucogenys	ENSNLEG00000014016	1 retrocopy	retro_nleu_1993 ,
Pongo abelii	ENSPPYG00000020619	1 retrocopy	retro_pabe_3666,
Pan troglodytes	ENSPTRG00000022170	1 retrocopy	retro_ptro_3139,